GoDaddy and Mac Mail not playing nice

In the past few weeks, I have an issue with GoDaddy emails in Mac Mail. When I receive an email, I read it, and then place it in a mailbox folder on the left taskbar. Later on, that email will reappear in my inbox, but a copy will still be in the mailbox where I dragged it earlier. If I delete from the inbox, a copy still remains in the mailbox. My inbox is now filling up. GoDaddy support said it was Apple. But when I tweeted them, they said it was a tricky problem they were working on. Which I doubt, since people have posted questions about this since last February in various online boards. Anyone have any idea what the issue is?